data_6PFE # _model_server_result.job_id WUmrUBr6EMmEPsQs9cYXzw _model_server_result.datetime_utc '2024-11-25 16:26:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6pfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":604}' # _entry.id 6PFE # _exptl.entry_id 6PFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.439 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHOTREXATE _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95 _cell.angle_gamma 90 _cell.entry_id 6PFE _cell.length_a 212.859 _cell.length_b 115.641 _cell.length_c 219.899 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G,H,I,J,K,L,M,Z,AA 1 1 C,E,N,O,P,Q,V,W,X,Y,BA,DA 2 1 D,R,S,T,U,CA 3 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_558 -x,y,-z+3 -1 0 0 0 1 0 0 0 -1 -57.496382 0 657.186654 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 M N N ? 5 Q N N ? 5 U N N ? 5 Y N N # _chem_comp.formula 'C20 H22 N8 O5' _chem_comp.formula_weight 454.439 _chem_comp.id MTX _chem_comp.mon_nstd_flag . _chem_comp.name METHOTREXATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 MTX doub 237 n y N1 C8A MTX sing 238 n y C2 NA2 MTX sing 239 n n C2 N3 MTX sing 240 n y NA2 HN21 MTX sing 241 n n NA2 HN22 MTX sing 242 n n N3 C4 MTX doub 243 n y C4 NA4 MTX sing 244 n n C4 C4A MTX sing 245 n y NA4 HN41 MTX sing 246 n n NA4 HN42 MTX sing 247 n n C4A N5 MTX sing 248 n y C4A C8A MTX doub 249 n y N5 C6 MTX doub 250 n y C6 C7 MTX sing 251 n y C6 C9 MTX sing 252 n n C7 N8 MTX doub 253 n y C7 H7 MTX sing 254 n n N8 C8A MTX sing 255 n y C9 N10 MTX sing 256 n n C9 H91 MTX sing 257 n n C9 H92 MTX sing 258 n n N10 CM MTX sing 259 n n N10 C14 MTX sing 260 n n CM HM1 MTX sing 261 n n CM HM2 MTX sing 262 n n CM HM3 MTX sing 263 n n C11 C12 MTX doub 264 n y C11 C16 MTX sing 265 n y C11 C MTX sing 266 n n C12 C13 MTX sing 267 n y C12 H12 MTX sing 268 n n C13 C14 MTX doub 269 n y C13 H13 MTX sing 270 n n C14 C15 MTX sing 271 n y C15 C16 MTX doub 272 n y C15 H15 MTX sing 273 n n C16 H16 MTX sing 274 n n C O MTX doub 275 n n C N MTX sing 276 n n N CA MTX sing 277 n n N HN MTX sing 278 n n CA CT MTX sing 279 n n CA CB MTX sing 280 n n CA HA MTX sing 281 n n CT O1 MTX doub 282 n n CT O2 MTX sing 283 n n O2 HO2 MTX sing 284 n n CB CG MTX sing 285 n n CB HB1 MTX sing 286 n n CB HB2 MTX sing 287 n n CG CD MTX sing 288 n n CG HG1 MTX sing 289 n n CG HG2 MTX sing 290 n n CD OE1 MTX doub 291 n n CD OE2 MTX sing 292 n n OE2 HOE2 MTX sing 293 n n # _atom_sites.entry_id 6PFE _atom_sites.fract_transf_matrix[1][1] 0.004698 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000411 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008647 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004565 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 2 NDP A 1 601 601 NDP NDP . G 3 UFP A 1 602 602 UFP UFP . H 4 OEA A 1 603 603 OEA T12 . I 5 MTX A 1 604 604 MTX MTX . J 2 NDP B 1 601 601 NDP NDP . K 3 UFP B 1 602 602 UFP UFP . L 4 OEA B 1 603 603 OEA T12 . M 5 MTX B 1 604 604 MTX MTX . N 2 NDP C 1 601 601 NDP NDP . O 3 UFP C 1 602 602 UFP UFP . P 4 OEA C 1 603 603 OEA T12 . Q 5 MTX C 1 604 604 MTX MTX . R 2 NDP D 1 601 601 NDP NDP . S 3 UFP D 1 602 602 UFP UFP . T 4 OEA D 1 603 603 OEA T12 . U 5 MTX D 1 604 604 MTX MTX . V 2 NDP E 1 601 601 NDP NDP . W 3 UFP E 1 602 602 UFP UFP . X 4 OEA E 1 603 603 OEA T12 . Y 5 MTX E 1 604 604 MTX MTX . Z 6 HOH A 1 701 29 HOH HOH . Z 6 HOH A 2 702 21 HOH HOH . Z 6 HOH A 3 703 40 HOH HOH . Z 6 HOH A 4 704 17 HOH HOH . Z 6 HOH A 5 705 15 HOH HOH . Z 6 HOH A 6 706 2 HOH HOH . Z 6 HOH A 7 707 20 HOH HOH . Z 6 HOH A 8 708 25 HOH HOH . Z 6 HOH A 9 709 3 HOH HOH . AA 6 HOH B 1 701 18 HOH HOH . AA 6 HOH B 2 702 31 HOH HOH . AA 6 HOH B 3 703 23 HOH HOH . AA 6 HOH B 4 704 16 HOH HOH . AA 6 HOH B 5 705 19 HOH HOH . AA 6 HOH B 6 706 8 HOH HOH . AA 6 HOH B 7 707 27 HOH HOH . AA 6 HOH B 8 708 4 HOH HOH . AA 6 HOH B 9 709 11 HOH HOH . AA 6 HOH B 10 710 30 HOH HOH . AA 6 HOH B 11 711 13 HOH HOH . AA 6 HOH B 12 712 1 HOH HOH . AA 6 HOH B 13 713 14 HOH HOH . AA 6 HOH B 14 714 34 HOH HOH . BA 6 HOH C 1 701 33 HOH HOH . BA 6 HOH C 2 702 43 HOH HOH . BA 6 HOH C 3 703 35 HOH HOH . BA 6 HOH C 4 704 39 HOH HOH . BA 6 HOH C 5 705 9 HOH HOH . CA 6 HOH D 1 701 22 HOH HOH . CA 6 HOH D 2 702 42 HOH HOH . CA 6 HOH D 3 703 5 HOH HOH . DA 6 HOH E 1 701 26 HOH HOH . DA 6 HOH E 2 702 32 HOH HOH . DA 6 HOH E 3 703 28 HOH HOH . DA 6 HOH E 4 704 36 HOH HOH . DA 6 HOH E 5 705 12 HOH HOH . DA 6 HOH E 6 706 10 HOH HOH . DA 6 HOH E 7 707 41 HOH HOH . DA 6 HOH E 8 708 24 HOH HOH . DA 6 HOH E 9 709 6 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 MTX . . . I 5 27.855 67.254 245.703 1 55.06 ? N1 MTX 604 A 1 HETATM 2 C C2 MTX . . . I 5 26.523 67.141 245.361 1 54.88 ? C2 MTX 604 A 1 HETATM 3 N NA2 MTX . . . I 5 25.885 68.168 244.811 1 57.79 ? NA2 MTX 604 A 1 HETATM 4 N N3 MTX . . . I 5 25.848 65.96 245.585 1 53.91 ? N3 MTX 604 A 1 HETATM 5 C C4 MTX . . . I 5 26.497 64.885 246.156 1 50.79 ? C4 MTX 604 A 1 HETATM 6 N NA4 MTX . . . I 5 25.844 63.738 246.327 1 53.28 ? NA4 MTX 604 A 1 HETATM 7 C C4A MTX . . . I 5 27.837 64.999 246.505 1 51.07 ? C4A MTX 604 A 1 HETATM 8 N N5 MTX . . . I 5 28.494 63.93 247.074 1 52.61 ? N5 MTX 604 A 1 HETATM 9 C C6 MTX . . . I 5 29.827 64.04 247.417 1 52.7 ? C6 MTX 604 A 1 HETATM 10 C C7 MTX . . . I 5 30.502 65.235 247.193 1 52.78 ? C7 MTX 604 A 1 HETATM 11 N N8 MTX . . . I 5 29.845 66.305 246.618 1 61.57 ? N8 MTX 604 A 1 HETATM 12 C C8A MTX . . . I 5 28.515 66.189 246.274 1 55.64 ? C8A MTX 604 A 1 HETATM 13 C C9 MTX . . . I 5 30.54 62.868 248.048 1 53.39 ? C9 MTX 604 A 1 HETATM 14 N N10 MTX . . . I 5 29.896 62.569 249.314 1 58.32 ? N10 MTX 604 A 1 HETATM 15 C CM MTX . . . I 5 28.913 61.473 249.345 1 40.19 ? CM MTX 604 A 1 HETATM 16 C C11 MTX . . . I 5 29.975 65.422 252.439 1 53.01 ? C11 MTX 604 A 1 HETATM 17 C C12 MTX . . . I 5 31.066 65.295 251.582 1 57.57 ? C12 MTX 604 A 1 HETATM 18 C C13 MTX . . . I 5 31.049 64.354 250.553 1 53.38 ? C13 MTX 604 A 1 HETATM 19 C C14 MTX . . . I 5 29.941 63.529 250.372 1 65.81 ? C14 MTX 604 A 1 HETATM 20 C C15 MTX . . . I 5 28.852 63.673 251.227 1 68.8 ? C15 MTX 604 A 1 HETATM 21 C C16 MTX . . . I 5 28.882 64.588 252.278 1 57.43 ? C16 MTX 604 A 1 HETATM 22 C C MTX . . . I 5 29.958 66.432 253.548 1 58.22 ? C MTX 604 A 1 HETATM 23 O O MTX . . . I 5 31.179 66.858 254.094 1 69.9 ? O MTX 604 A 1 HETATM 24 N N MTX . . . I 5 28.78 66.894 253.97 1 64.62 ? N MTX 604 A 1 HETATM 25 C CA MTX . . . I 5 28.582 67.869 255.029 1 64.3 ? CA MTX 604 A 1 HETATM 26 C CT MTX . . . I 5 27.2 67.759 255.594 1 66.01 ? CT MTX 604 A 1 HETATM 27 O O1 MTX . . . I 5 26.361 67.043 255.011 1 63.61 ? O1 MTX 604 A 1 HETATM 28 O O2 MTX . . . I 5 26.874 68.377 256.633 1 66.86 ? O2 MTX 604 A 1 HETATM 29 C CB MTX . . . I 5 28.766 69.281 254.49 1 59.23 ? CB MTX 604 A 1 HETATM 30 C CG MTX . . . I 5 29.222 70.24 255.58 1 71.28 ? CG MTX 604 A 1 HETATM 31 C CD MTX . . . I 5 29.246 71.654 255.048 1 77.59 ? CD MTX 604 A 1 HETATM 32 O OE1 MTX . . . I 5 28.425 72.502 255.464 1 72.08 ? OE1 MTX 604 A 1 HETATM 33 O OE2 MTX . . . I 5 30.112 72 254.214 1 74.89 ? OE2 MTX 604 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #